---
name: "obisilva"
section: "1"
platform: "linux"
package: "obitools"
version: "1.2.12+dfsg-2"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/obisilva"
---

# obisilva(1)

description of obisilva obisilva: converts and optionally download the Silva database into an ecoPCR database. The formated database include the taxonomy as defined by the Silva authors. WARNING:

## NAME

obisilva - description of obisilva

*obisilva*: converts and optionally download the *Silva database* into an ecoPCR database. The formated database include the taxonomy as defined by the Silva authors.

**WARNING:**

Take care that the numeric taxids associated to the sequences are specific  to this Silva database and not compatible with the NCBI taxids.  The taxids present in a version of the Silva database (*i.e* ssu, lsu, parc, ref…) are are just valid for this version of the database and not compatible  with the taxids used in another version.

## OBISILVA SPECIFIC OPTIONS

- **-s, --ssu**

  Specify that you are interested in the **SSU** database.

  *Example:*

  ```
  > obisilva --ssu --parc
  ```

  This download and format into an ecoPCR database the latest version of the **SSUParc** database of **Silva**.

- **-l, --lsu**

  Specify that you are interested in the **LSU** database.

  *Example:*

  ```
  > obisilva --ssu --parc
  ```

  This download and format into an ecoPCR database the latest version of the **LSUParc** database of **Silva**.

- **-p, --parc**

  Specify that you are interested in the **Parc** (complete) version of the **Silva** database.

- **-r, --ref**

  Specify that you are interested in the **Reference** (cleaned to keep only high quality sequences) version of the **Silva** database.

- **-n, --nr**

  Specify that you are interested in the **Non redundant** version of the **Silva** database. just a version of the to closely related sequence is kept in this version of the database

  **WARNING:**

  Non redundant version of **Silva** exists only for the SSU sequences in its **Reference** and  **Truncated** version

- **-t, --trunc**

  Specify that you are interested in the **Truncated** (limited to the rDNA element without flanked regions) version of the **Silva** database.

- **--local=\<DIRNAME\>**

  Specify you have already downloaded a copy of the **Silva** database located at the following URL *http://www.arb-\*\*Silva\*\*.de/no\_cache/download/archive/current/Exports/*

  *Example:*

  ```
  > obisilva --ssu --parc --local=**Silva**Dir
  ```

  This format the **SSUParc** version of the **Silva** database pre-downloaded in the *\*\*Silva\*\*Dir* directory.

## COMMON OPTIONS

- **-h, --help**

  Shows this help message and exits.

- **--DEBUG**

  Sets logging in debug mode.

## AUTHOR

The OBITools Development Team - LECA

## COPYRIGHT

2019 - 2015, OBITool Development Team